.command.sh - Workdir - NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (COLO829_tumor_10pct_rep2;manta_fusion)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/ba7ac72f82ffbeb2d7c2d8a088fc02/.command.sh
Size: 428 bytes
Task: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (COLO829_tumor_10pct_rep2;manta_fusion)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools stats \
     \
     \
     \
     \
     \
     \
    COLO829_tumor_10pct_rep2.manta_fusion.somatic_sv.scored.vcf.gz > COLO829_tumor_10pct_rep2.manta_fusion.somatic_sv.scored.bcftools_stats.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS":
    bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
END_VERSIONS